Methanotrophic bacteria are defined by their ability to use methane as their sole source of carbon and energy under ambient conditions. This ability, in conjunction with the abundance of methane, makes the biotransformation of methane a potentially unique and valuable process. As such, several approaches have been used in attempts to harnesss the unique natural abilities of these organisms for commercial applications.
Historically, the commercial applications of biotransformation of methane have fallen broadly into three categories:                1) Production of single cell protein (Sharpe D. H. BioProtein Manufacture (1989). Ellis Horwood series in applied science and industrial technology. New York: Halstead Press) (Villadsen, John, Recent Trends Chem. React. Eng., [Proc. Int. Chem. React. Eng. Conf.], 2nd (1987), Volume 2, pp 320–33. Editor(s): Kulkarni, B. D.; Mashelkar, R. A.; Sharma, M. M. Publisher: Wiley East., New Delhi, India; Naguib, M., Proc. OAPEC Symp. Petroprotein, [Pap.] (1980), Meeting Date 1979, pp 253–77 Publisher: Organ. Arab Pet. Exporting Countries, Kuwait, Kuwait);        
2) Epoxidation of alkenes for production of chemicals (U.S. Pat. No. 4,348,476); and
3) Biodegradation of chlorinated pollutants (Tsien et al., Gas, Oil, Coal, Environ. Biotechnol. 2, [Pap. Int. IGT Symp. Gas, Oil, Coal, Environ. Biotechnol.], 2nd (1990), pp 83–104. Editor(s): Akin, Cavit; Smith, Jared. Publisher: Inst. Gas Technol., Chicago, Ill.; WO 9,633,821; Merkley et al., Biorem. Recalcitrant Org., [Pap. Int. In Situ On-Site Bioreclam. Symp.], 3rd (1995), pp. 165–74. Editor(s): Hinchee, Robert E; Anderson, Daniel B.; Hoeppel, Ronald E. Publisher: Battelle Press, Columbus, Ohio; Meyer et al., Microb. Releases 2(1): 11–22 (1993)).
Epoxidation of alkenes has experienced only slight commercial success due to low product yields, toxicity of products and the large amount of cell mass required to generate products.
Large-scale protein production from methane, termed single cell protein or SCP, has been technically feasible and commercialized at large scale (Villadsen, supra). Single cell protein is a relatively low value product. As such, the economic production cannot tolerate heavy bioprocessing costs. The yield of the methanotrophic strain used for producing SCP may be critical to the overall economic viability of the process. Microbial biomass produced by methanotrophic bacteria is typically very high in protein content (˜70–80% by weight), which can restrict the direct use of this protein to certain types of animal feed.
In addition to the synthesis of SCP, methanotrophic cells can further build the oxidation products of methane (i.e. methanol and formaldehyde) into complex molecules such as carbohydrates and lipids. For example, under certain conditions methanotrophs are known to produce exopolysaccharides (WO 02/20797; WO 02/20728; Ivanova et al., Mikrobiologiya 57(4):600–5 (1988); Kilbane, John J., II Gas, Oil, Coal, Environ. Biotechnol. 3, [Pap. IGT's Int. Symp.], 3rd (1991), Meeting Date 1990, pp. 207–26. Editor(s): Akin, Cavit; Smith, Jared. Publisher: IGT, Chicago, Ill.). Similarly, methanotrophs are known to accumulate both isoprenoid compounds and carotenoid pigments of various carbon lengths (WO 02/20733; WO 02/20728; Urakami et al., J. Gen. Appl. Microbiol. 32(4):317–41 (1986)).
Most recently, the natural abilities of methanotrophic organisms have been stretched by the advances of genetic engineering. Odom et al. have investigated Methyolomonas sp. 16a as a microbial platform of choice for production of a variety of materials beyond single cell protein including carbohydrates, pigments, terpenoid compounds and aromatic compounds (WO 02/20728; WO 02/18617). This particular methanotrophic bacterial strain is capable of efficiently using either methanol or methane as a carbon substrate, is metabolically versatile in that it contains multiple pathways for the incorporation of carbon from formaldehyde into 3-carbon units, and is amenable to genetic engineering via bacterial conjugation using donor species such as Escherichia coli. Thus, Methyolomonas sp. 16a can be engineered to produce new classes of products other than those naturally produced from methane. Further advancement in the metabolic engineering of methanotrophs such as Methyolomonas sp. 16a, however, is currently limited by the lack of a detailed understanding of promoters useful to drive the expression of foreign and native genes in this host. Additionally, it would be useful to possess a suite of promoters that are individually regulatable under a variety of natural growth and induction conditions.
In general, prokaryotic promoters can play an important role in biotechnology, particularly for directing expression of chimeric genes to alter cellular metabolism to produce larger quantities of a natural productor new products. Producing high levels of a specific protein may also be desirable as a product. Promoters that are generally used for gene expression in E. coli may not be suitable for driving chimeric gene expression in Methylomonas, especially when a strong or inducible promoter is required. Promoters that are strong in E. coli, generally have much lower expression levels in Methylomonas. Induction systems used with inducible promoters in E. coli generally do not function well in Methylomonas. 
The problem to be solved therefore is to provide promoters that are useful for expression of chimeric genes under desired conditions in Methylomonas. Promoters with high expression during growth on methane and methanol are valuable when Methylomonas is used as a production host. Similarly, promoters induced by growth on nitrate and by change in temperature and pH conditions are very applicable in industrial settings, as each of these conditions can be adjusted easily. Applicants have solved the stated problem by identifying genes within the Methylomonas sp. 16a genome that are regulated by designated metabolic and growth conditions, and isolating the promoters from these genes. The nucleic acid sequences of the genes can be used for bioreactor monitoring in Methylomonas sp. and C1 metabolizing bacterial cultures. Specifically, applicants have used microarray technology to identify genes that are responsive to: 1.) growth on methane and methanol; 2.) induction in the presence of nitrate; 3.) induction by change in growth temperature; and 4.) induction by modification of media pH. Homologs of these genes should be useful for similar purposes in a variety of C1 metabolizing bacteria.